*/
package jalview.bin;
+import java.awt.GraphicsEnvironment;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
-import java.util.Hashtable;
import java.util.Map;
import java.util.Vector;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignViewportI;
-import jalview.api.JalviewApp;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
-import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.IdentifyFile;
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
-import jalview.javascript.JSFunctionExec;
-import jalview.javascript.MouseOverStructureListener;
-import jalview.renderer.seqfeatures.FeatureRenderer;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.structure.SelectionSource;
-import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
-import netscape.javascript.JSObject;
/**
* Main class for Jalview Application <br>
* @author $author$
* @version $Revision$
*/
-public class Jalview implements JalviewJSApi
+public class Jalview implements ApplicationSingletonI
{
- static
+
+ // for testing those nasty messages you cannot ever find.
+ // static
+ // {
+ // System.setOut(new PrintStream(new ByteArrayOutputStream())
+ // {
+ // @Override
+ // public void println(Object o)
+ // {
+ // if (o != null)
+ // {
+ // System.err.println(o);
+ // }
+ // }
+ //
+ // });
+ // }
+ public static Jalview getInstance()
{
- Platform.getURLCommandArguments();
+ return (Jalview) ApplicationSingletonProvider
+ .getInstance(Jalview.class);
}
- private boolean headless;
-
- // singleton instance of this class
+ private Jalview()
+ {
+ }
- private static Jalview instance;
+ private boolean headless;
private Desktop desktop;
- public static AlignFrame currentAlignFrame;
-
- public boolean isJavaAppletTag;
+ public AlignFrame currentAlignFrame;
public String appletResourcePath;
- JalviewAppLoader appLoader;
-
- protected JSFunctionExec jsFunctionExec;
+ public String j2sAppletID;
private boolean noCalculation, noMenuBar, noStatus;
static
{
- if (!Platform.isJS())
- /**
- * Java only
- *
- * @j2sIgnore
- */
+ if (Platform.isJS()) {
+ Platform.getURLCommandArguments();
+ } else /** @j2sIgnore */
{
// grab all the rights we can for the JVM
Policy.setPolicy(new Policy()
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch processing
- * events.
+ * TODO: generalise to track all jalview events to orchestrate batch
+ * processing events.
*/
private int queued = 0;
}
- public static Jalview getInstance()
- {
- return instance;
- }
-
-
private final static boolean doPlatformLogging = false;
/**
{
Platform.startJavaLogging();
}
-
- instance = new Jalview();
- instance.doMain(args);
+ getInstance().doMain(args);
}
/**
{
boolean isJS = Platform.isJS();
- if (isJS)
- {
- Platform.setAppClass(this);
- }
- else
+ if (!isJS)
{
System.setSecurityManager(null);
}
+ /*
+ * @j2sNative J2S.db._DirectDatabaseCalls["compbio.dundee.ac.uk"]=null;
+ * @j2sNative J2S.db._DirectDatabaseCalls["jalview.org"]=null;
+ *
+ */
System.out
.println("Java version: " + System.getProperty("java.version"));
System.out.println("Java Home: " + System.getProperty("java.home"));
}
// report Jalview version
- Cache.loadBuildProperties(true);
+ Cache.getInstance().loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
headless = false;
Cache.loadProperties(usrPropsFile); // must do this before
+ boolean allowServices = true;
+
if (isJS)
{
- isJavaAppletTag = aparser.isApplet();
- if (isJavaAppletTag)
- {
- Preferences.setAppletDefaults();
- Cache.loadProperties(usrPropsFile); // again, because we
- // might be changing defaults here?
- }
- System.out.println(
- "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
- appletResourcePath = aparser.getValue("Info.resourcePath");
+ j2sAppletID = Platform.getAppID(null);
+ Preferences.setAppletDefaults();
+ Cache.loadProperties(usrPropsFile); // again, because we
+ // might be changing defaults here?
+ appletResourcePath = (String) aparser.getAppletValue("resourcepath",
+ null, true);
}
else
/**
showUsage();
System.exit(0);
}
- // ?>>
+ // BH note: Only -nodisplay is official; others are deprecated?
if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
+ || aparser.contains("headless")
+ || GraphicsEnvironment.isHeadless())
{
- System.setProperty("java.awt.headless", "true");
+ if (!isJS) {
+ // BH Definitely not a good idea in JavaScript;
+ // probably should not be here for Java, either.
+ System.setProperty("java.awt.headless", "true");
+ }
headless = true;
}
- // <<?
-
- // anything else!
final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
- if (jabawsUrl != null)
+ allowServices = !("none".equals(jabawsUrl));
+ if (allowServices && jabawsUrl != null)
{
try
{
}
defs = aparser.getValue("setprop");
}
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
- {
- headless = true;
- }
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
try
System.exit(0);
}
- desktop = null;
-
if (!isJS)
/** @j2sIgnore */
{
* configure 'full' SO model if preferences say to, else use the default (full SO)
* - as JS currently doesn't have OBO parsing, it must use 'Lite' version
*/
- boolean soDefault = !Platform.isJS();
+ boolean soDefault = !isJS;
if (Cache.getDefault("USE_FULL_SO", soDefault))
{
- SequenceOntologyFactory.setInstance(new SequenceOntology());
+ SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
}
+
+ desktop = null;
if (!headless)
{
- desktop = new Desktop();
+ desktop = Desktop.getInstance();
desktop.setInBatchMode(true); // indicate we are starting up
-
try
{
JalviewTaskbar.setTaskbar(this);
{
System.out.println("Error setting Taskbar: " + t.getMessage());
}
-
desktop.setVisible(true);
-
- if (!Platform.isJS())
+ if (Platform.isJS())
+ Cache.setProperty("SHOW_JWS2_SERVICES", "false");
+ if (allowServices)
+ {
+ desktop.startServiceDiscovery();
+ }
+ if (!isJS)
/**
* Java only
*
* @j2sIgnore
*/
{
- desktop.startServiceDiscovery();
if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
BioJsHTMLOutput.updateBioJS();
}
}
-
parseArguments(aparser, true);
}
/**
- * Allow an outside entity to initiate the second half of argument parsing
- * (only).
+ * Parse all command-line String[] arguments as well as all JavaScript-derived
+ * parameters from Info.
*
- * @param args
- * @return null is good
- */
- @Override
- public Object parseArguments(String[] args)
- {
-
- try
- {
- parseArguments(new ArgsParser(args), false);
- return null;
- } catch (Throwable t)
- {
- return t;
- }
- }
-
- /**
+ * We allow for this method to be run from JavaScript. Basically allowing
+ * simple scripting.
*
* @param aparser
* @param isStartup
*/
- private void parseArguments(ArgsParser aparser, boolean isStartup)
+ public void parseArguments(ArgsParser aparser, boolean isStartup)
{
String groovyscript = null; // script to execute after all loading is
String file = aparser.getValue("open", true);
- if (file == null && desktop == null)
+ if (!isJS && file == null && desktop == null)
{
System.out.println("No files to open!");
System.exit(1);
}
+ setDisplayParameters(aparser);
+
+ // time to open a file.
+
long progress = -1;
DataSourceType protocol = null;
FileLoader fileLoader = new FileLoader(!headless);
FileFormatI format = null;
// Finally, deal with the remaining input data.
- if (file != null)
+ AlignFrame af = null;
+
+ JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null);
+
+ if (file == null)
+ {
+ if (isJS)
+ {
+ // JalviewJS allows sequence1 sequence2 ....
+
+ }
+ else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+
+ // We'll only open the default file if the desktop is visible.
+ // And the user
+ // ////////////////////
+
+ file = Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/examples/exampleFile_2_7.jar");
+ if (file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ {
+ // hardwire upgrade of the startup file
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
+ Cache.removeProperty("STARTUP_FILE");
+ }
+
+ protocol = DataSourceType.FILE;
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = DataSourceType.URL;
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ format = FileFormat.Jalview;
+ }
+ else
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ // TODO what?
+ }
+ }
+ af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+ }
+ }
+ else
{
if (!headless)
{
}
}
}
- String fileFormat = (isJavaAppletTag
- ? aparser.getAppletValue("format", null)
+
+ String fileFormat = (isJS
+ ? (String) aparser.getAppletValue("format", null, true)
: null);
protocol = AppletFormatAdapter.checkProtocol(file);
try
{
- format = (isJavaAppletTag && fileFormat != null
+ format = (fileFormat != null
? FileFormats.getInstance().forName(fileFormat)
: null);
if (format == null)
{
format = new IdentifyFile().identify(file, protocol);
}
- format = new IdentifyFile().identify(file, protocol);
} catch (FileFormatException e1)
{
// TODO ?
}
- if (aparser.contains(ArgsParser.NOMENUBAR))
- {
- noMenuBar = true;
- System.out.println("CMD [nomenu] executed successfully!");
- }
-
- if (aparser.contains(ArgsParser.NOSTATUS))
- {
- noStatus = true;
- System.out.println("CMD [nostatus] executed successfully!");
- }
-
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
- {
- noAnnotation = true;
- System.out.println("CMD no-annotation executed successfully!");
- }
- if (aparser.contains(ArgsParser.NOCALCULATION))
- {
- noCalculation = true;
- System.out.println("CMD [nocalculation] executed successfully!");
- }
-
- AlignFrame af = new FileLoader(!headless).LoadFileWaitTillLoaded(file,
- protocol, format);
+ af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol,
+ format);
if (af == null)
{
- System.out.println("error");
+ System.out.println("jalview error - AlignFrame was not created");
}
else
{
}
setCurrentAlignFrame(af);
- String data = aparser.getValue(ArgsParser.COLOUR, true);
- if (data != null)
- {
- data.replaceAll("%20", " ");
-
- ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
- af.getViewport(), af.getViewport().getAlignment(), data);
-
- if (cs != null)
- {
- System.out.println(
- "CMD [-color " + data + "] executed successfully!");
- }
- af.changeColour(cs);
- }
-
- // Must maintain ability to use the groups flag
- data = aparser.getValue(ArgsParser.GROUPS, true);
- if (data != null)
- {
- af.parseFeaturesFile(data,
- AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
- "CMD groups[-" + data + "] executed successfully!");
- }
- data = aparser.getValue(ArgsParser.FEATURES, true);
- if (data != null)
- {
- af.parseFeaturesFile(data,
- AppletFormatAdapter.checkProtocol(data));
- // System.out.println("Added " + data);
- System.out.println(
- "CMD [-features " + data + "] executed successfully!");
- }
- data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
- if (data != null)
- {
- af.loadJalviewDataFile(data, null, null, null);
- // System.out.println("Added " + data);
- System.out.println(
- "CMD [-annotations " + data + "] executed successfully!");
- }
-
- // JavaScript feature
-
- if (aparser.contains(ArgsParser.SHOWOVERVIEW))
- {
- af.overviewMenuItem_actionPerformed(null);
- System.out.println("CMD [showoverview] executed successfully!");
- }
-
- // set or clear the sortbytree flag.
- if (aparser.contains(ArgsParser.SORTBYTREE))
- {
- af.getViewport().setSortByTree(true);
- if (af.getViewport().getSortByTree())
- {
- System.out.println("CMD [-sortbytree] executed successfully!");
- }
- }
-
- boolean doUpdateAnnotation = false;
- /**
- * we do this earlier in JalviewJS because of a complication with
- * SHOWOVERVIEW
- *
- * For now, just fixing this in JalviewJS.
- *
- *
- * @j2sIgnore
- *
- */
- {
- if (aparser.contains(ArgsParser.NOANNOTATION)
- || aparser.contains(ArgsParser.NOANNOTATION2))
- {
- af.getViewport().setShowAnnotation(false);
- if (!af.getViewport().isShowAnnotation())
- {
- doUpdateAnnotation = true;
- System.out
- .println("CMD no-annotation executed successfully!");
- }
- }
- }
+ setFrameDependentProperties(aparser, af);
-
- if (aparser.contains(ArgsParser.NOSORTBYTREE))
- {
- af.getViewport().setSortByTree(false);
- if (!af.getViewport().getSortByTree())
- {
- doUpdateAnnotation = true;
- System.out
- .println("CMD [-nosortbytree] executed successfully!");
- }
- }
- if (doUpdateAnnotation)
- { // BH 2019.07.24
- af.setMenusForViewport();
- af.alignPanel.updateLayout();
- }
-
- data = aparser.getValue(ArgsParser.TREE, true);
- if (data != null)
- {
- try
- {
- System.out.println(
- "CMD [-tree " + data + "] executed successfully!");
- NewickFile nf = new NewickFile(data,
- AppletFormatAdapter.checkProtocol(data));
- af.getViewport()
- .setCurrentTree(af.showNewickTree(nf, data).getTree());
- } catch (IOException ex)
- {
- System.err.println("Couldn't add tree " + data);
- ex.printStackTrace(System.err);
- }
- }
- // TODO - load PDB structure(s) to alignment JAL-629
- // (associate with identical sequence in alignment, or a specified
- // sequence)
- if (isJavaAppletTag)
+ if (isJS)
{
- loadAppletParams(aparser, af);
+ jsApp.initFromParams(af);
}
- else if (!isJS)
+ else
/**
* Java only
*
groovyscript = null;
}
}
- createOutputFiles(aparser, af, format);
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
+ if (!isJS || !isStartup) {
+ createOutputFiles(aparser, format);
}
}
- }
-
-
- AlignFrame startUpAlframe = null;
- // We'll only open the default file if the desktop is visible.
- // And the user
- // ////////////////////
-
- if (!isJS && !headless && file == null
- && Cache.getDefault("SHOW_STARTUP_FILE", true))
- /**
- * Java only
- *
- * @j2sIgnore
- */
- {
- file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
- {
- // hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
- // and remove the stale setting
- Cache.removeProperty("STARTUP_FILE");
- }
-
- protocol = DataSourceType.FILE;
-
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
-
- if (file.endsWith(".jar"))
- {
- format = FileFormat.Jalview;
- }
- else
+ if (headless)
{
- try
- {
- format = new IdentifyFile().identify(file, protocol);
- } catch (FileFormatException e)
- {
- // TODO what?
- }
+ af.getViewport().getCalcManager().shutdown();
}
-
- startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
- format);
-
}
-
// extract groovy arguments before anything else.
// Once all other stuff is done, execute any groovy scripts (in order)
- if (groovyscript != null)
+ if (!isJS && groovyscript != null)
{
if (Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, startUpAlframe);
+ executeGroovyScript(groovyscript, af);
}
else
{
}
desktop.setInBatchMode(false);
}
+
+ if (jsApp != null) {
+ jsApp.callInitCallback();
+ }
}
-
+
/**
- * Writes an output file for each format (if any) specified in the
- * command-line arguments. Supported formats are currently
- * <ul>
- * <li>png</li>
- * <li>svg</li>
- * <li>html</li>
- * <li>biojsmsa</li>
- * <li>imgMap</li>
- * <li>eps</li>
- * </ul>
- * A format parameter should be followed by a parameter specifying the output
- * file name. {@code imgMap} parameters should follow those for the
- * corresponding alignment image output.
+ * Set general display parameters irrespective of file loading or headlessness.
*
* @param aparser
- * @param af
- * @param format
*/
- private void createOutputFiles(ArgsParser aparser, AlignFrame af,
- FileFormatI format)
+ private void setDisplayParameters(ArgsParser aparser)
{
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+ if (aparser.contains(ArgsParser.NOMENUBAR))
{
- String outputFormat = aparser.nextValue();
- String file = aparser.nextValue();
+ noMenuBar = true;
+ System.out.println("CMD [nomenu] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOSTATUS))
+ {
+ noStatus = true;
+ System.out.println("CMD [nostatus] executed successfully!");
+ }
+
+ if (aparser.contains(ArgsParser.NOANNOTATION)
+ || aparser.contains(ArgsParser.NOANNOTATION2))
+ {
+ noAnnotation = true;
+ System.out.println("CMD no-annotation executed successfully!");
+ }
+ if (aparser.contains(ArgsParser.NOCALCULATION))
+ {
+ noCalculation = true;
+ System.out.println("CMD [nocalculation] executed successfully!");
+ }
+ }
+
- if (outputFormat.equalsIgnoreCase("png"))
+ private void setFrameDependentProperties(ArgsParser aparser,
+ AlignFrame af)
+ {
+ String data = aparser.getValue(ArgsParser.COLOUR, true);
+ if (data != null)
+ {
+ data.replaceAll("%20", " ");
+
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
+
+ if (cs != null)
{
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
+ System.out.println(
+ "CMD [-color " + data + "] executed successfully!");
}
- else if (outputFormat.equalsIgnoreCase("svg"))
+ af.changeColour(cs);
+ }
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue(ArgsParser.GROUPS, true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD groups[-" + data + "] executed successfully!");
+ }
+ data = aparser.getValue(ArgsParser.FEATURES, true);
+ if (data != null)
+ {
+ af.parseFeaturesFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-features " + data + "] executed successfully!");
+ }
+ data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data, null, null, null);
+ // System.out.println("Added " + data);
+ System.out.println(
+ "CMD [-annotations " + data + "] executed successfully!");
+ }
+
+ // JavaScript feature
+
+ if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+ {
+ af.overviewMenuItem_actionPerformed(null);
+ System.out.println("CMD [showoverview] executed successfully!");
+ }
+
+ // set or clear the sortbytree flag.
+ if (aparser.contains(ArgsParser.SORTBYTREE))
+ {
+ af.getViewport().setSortByTree(true);
+ if (af.getViewport().getSortByTree())
{
- File imageFile = new File(file);
- imageName = imageFile.getName();
- af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
- continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
- System.out.println("Creating HTML image: " + file);
- continue;
+ System.out.println("CMD [-sortbytree] executed successfully!");
}
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+ }
+
+ boolean doUpdateAnnotation = false;
+ /**
+ * we do this earlier in JalviewJS because of a complication with
+ * SHOWOVERVIEW
+ *
+ * For now, just fixing this in JalviewJS.
+ *
+ *
+ * @j2sIgnore
+ *
+ */
+ {
+ if (noAnnotation)
{
- if (file == null)
+ af.getViewport().setShowAnnotation(false);
+ if (!af.getViewport().isShowAnnotation())
{
- System.err.println("The output html file must not be null");
- return;
+ doUpdateAnnotation = true;
}
+ }
+ }
+
+ if (aparser.contains(ArgsParser.NOSORTBYTREE))
+ {
+ af.getViewport().setSortByTree(false);
+ if (!af.getViewport().getSortByTree())
+ {
+ doUpdateAnnotation = true;
+ System.out
+ .println("CMD [-nosortbytree] executed successfully!");
+ }
+ }
+ if (doUpdateAnnotation)
+ { // BH 2019.07.24
+ af.setMenusForViewport();
+ af.alignPanel.updateLayout();
+ }
+
+ data = aparser.getValue(ArgsParser.TREE, true);
+ if (data != null)
+ {
+ try
+ {
+ NewickFile nf = new NewickFile(data,
+ AppletFormatAdapter.checkProtocol(data));
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, data).getTree());
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
+ }
+ }
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
+
+ }
+
+ /**
+ * Writes an output file for each format (if any) specified in the
+ * command-line arguments. Supported formats are currently
+ * <ul>
+ * <li>png</li>
+ * <li>svg</li>
+ * <li>html</li>
+ * <li>biojsmsa</li>
+ * <li>imgMap</li>
+ * <li>eps</li>
+ * </ul>
+ * A format parameter should be followed by a parameter specifying the output
+ * file name. {@code imgMap} parameters should follow those for the
+ * corresponding alignment image output.
+ *
+ * @param aparser
+ * @param format
+ */
+ private void createOutputFiles(ArgsParser aparser, FileFormatI format)
+ {
+ AlignFrame af = currentAlignFrame;
+ while (aparser.getSize() >= 2)
+ {
+ String outputFormat = aparser.nextValue();
+ File imageFile;
+ String fname;
+ switch (outputFormat.toLowerCase())
+ {
+ case "png":
+ imageFile = new File(aparser.nextValue());
+ af.createPNG(imageFile);
+ System.out.println(
+ "Creating PNG image: " + imageFile.getAbsolutePath());
+ continue;
+ case "svg":
+ imageFile = new File(aparser.nextValue());
+ af.createSVG(imageFile);
+ System.out.println(
+ "Creating SVG image: " + imageFile.getAbsolutePath());
+ continue;
+ case "eps":
+ imageFile = new File(aparser.nextValue());
+ System.out.println(
+ "Creating EPS file: " + imageFile.getAbsolutePath());
+ af.createEPS(imageFile);
+ continue;
+ case "biojsmsa":
+ fname = new File(aparser.nextValue()).getAbsolutePath();
try
{
BioJsHTMLOutput.refreshVersionInfo(
e.printStackTrace();
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
+ bjs.exportHTML(fname);
+ System.out.println("Creating BioJS MSA Viwer HTML file: " + fname);
continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
+ case "html":
+ fname = new File(aparser.nextValue()).getAbsolutePath();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fname);
+ System.out.println("Creating HTML image: " + fname);
continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
+ case "imgmap":
+ imageFile = new File(aparser.nextValue());
+ af.alignPanel.makePNGImageMap(imageFile, "unnamed.png");
System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
+ "Creating image map: " + imageFile.getAbsolutePath());
continue;
+ default:
+ // fall through - try to parse as an alignment data export format
+ FileFormatI outFormat = null;
+ try
+ {
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
+ {
+ }
+ if (outFormat == null)
+ {
+ System.out.println("Couldn't parse " + outputFormat
+ + " as a valid Jalview format string.");
+ continue;
+ }
+ if (!outFormat.isWritable())
+ {
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ continue;
+ }
+ // record file as it was passed to Jalview so it is recognisable to the CLI
+ // caller
+ String file;
+ fname = new File(file = aparser.nextValue()).getAbsolutePath();
+ // JBPNote - yuck - really wish we did have a bean returned from this which gave
+ // success/fail like before !
+ af.saveAlignment(fname, outFormat);
+ if (!af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in " + outputFormat
+ + " format to " + file);
+ continue;
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + outputFormat + " format!!");
+ }
}
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
- {
- System.out.println(
- "Written alignment in " + format + " format to " + file);
- }
- else
- {
- System.out.println("Error writing file " + file + " in " + format
- + " format!!");
- }
-
}
-
+ // ??? Should report - 'ignoring' extra args here...
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Ignoring extra argument: " + aparser.nextValue());
+ }
}
private static void showUsage()
/**
* start a User Config prompt asking if we can log usage statistics.
*/
- PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
+ PromptUserConfig prompter = new PromptUserConfig(Desktop.getDesktopPane(),
"USAGESTATS", "Jalview Usage Statistics",
"Do you want to help make Jalview better by enabling "
+ "the collection of usage statistics with Google Analytics ?"
public static AlignFrame getCurrentAlignFrame()
{
- return Jalview.currentAlignFrame;
+ return Jalview.getInstance().currentAlignFrame;
}
public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- Jalview.currentAlignFrame = currentAlignFrame;
- }
-
- /**
- * Get the SwingJS applet ID and combine that with the frameType
- *
- * @param frameType
- * "alignment", "desktop", etc., or null
- * @return
- */
- public static String getAppID(String frameType)
- {
- String id = Cache.getProperty("Info.j2sAppletID");
- if (id == null)
- {
- id = "jalview";
- }
- return id + (frameType == null ? "" : "-" + frameType);
- }
-
- /**
- * Handle all JalviewLite applet parameters
- *
- * @param aparser
- * @param af
- */
- private void loadAppletParams(ArgsParser aparser, AlignFrame af)
- {
- JalviewApp app = new JalviewApp()
- {
-
- // TODO BH 2019
- //
- // These are methods that are in JalviewLite that various classes call
- // but are not in JalviewLiteJsApi. Or, even if they are, other classes
- // call
- // them to JalviewLite directly. Some may not be necessary, but they have
- // to
- // be at least mentioned here, or the classes calling them should
- // reference
- // JalviewLite itself.
-
- private boolean alignPDBStructures; // From JalviewLite; not implemented
-
- private Hashtable<String, Hashtable<String, String[]>> jsmessages;
-
- private Hashtable<String, int[]> jshashes;
-
- @Override
- public String getParameter(String name)
- {
- return aparser.getAppletValue(name, null);
- }
-
- @Override
- public boolean getDefaultParameter(String name, boolean def)
- {
- String stn;
- return ((stn = getParameter(name)) == null ? def
- : "true".equalsIgnoreCase(stn));
- }
-
- /**
- * Get the applet-like document base even though this is an application.
- */
- @Override
- public URL getDocumentBase()
- {
- return Platform.getDocumentBase();
- }
-
- /**
- * Get the applet-like code base even though this is an application.
- */
- @Override
- public URL getCodeBase()
- {
- return Platform.getCodeBase();
- }
-
- @Override
- public AlignViewportI getViewport()
- {
- return af.getViewport();
- }
-
- /**
- * features
- *
- */
- @Override
- public boolean parseFeaturesFile(String filename,
- DataSourceType protocol)
- {
- return af.parseFeaturesFile(filename, protocol);
- }
-
- /**
- * scorefile
- *
- */
- @Override
- public boolean loadScoreFile(String sScoreFile) throws IOException
- {
- af.loadJalviewDataFile(sScoreFile, null, null, null);
- return true;
- }
-
- /**
- * annotations, jpredfile, jnetfile
- *
- */
- @Override
- public void updateForAnnotations()
- {
- af.updateForAnnotations();
- }
-
- @Override
- public void loadTree(NewickFile fin, String treeFile)
- throws IOException
- {
- // n/a -- already done by standard Jalview command line processing
- }
-
- @Override
- public void setAlignPdbStructures(boolean defaultParameter)
- {
- alignPDBStructures = true;
- }
-
- @Override
- public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
- String[] chains, DataSourceType protocol)
- {
- StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs);
- }
-
- @Override
- public void setFeatureGroupState(String[] groups, boolean state)
- {
- af.setFeatureGroupState(groups, state);
- }
-
- @Override
- public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
- String[][] chains, String[] protocols)
- {
- System.err.println(
- "Jalview applet interface alignedStructureView not implemented");
- }
-
- @Override
- public void newFeatureSettings()
- {
- System.err.println(
- "Jalview applet interface newFeatureSettings not implemented");
- }
-
- private Vector<Runnable> jsExecQueue;
-
- @Override
- public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
- {
- jsFunctionExec = exec;
- return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
- : jsExecQueue);
- }
-
-// AppletContext deprecated
-//
-// @Override
-// public AppletContext getAppletContext()
-// {
-// // TODO Auto-generated method stub
-// return null;
-// }
-//
- @Override
- public boolean isJsfallbackEnabled()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public JSObject getJSObject()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
- {
- // TODO Q: what exactly is this? BH
- return null;
- }
-
- @Override
- public void updateColoursFromMouseOver(Object source,
- MouseOverStructureListener mouseOverStructureListener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Object[] getSelectionForListener(SequenceGroup seqsel,
- ColumnSelection colsel, HiddenColumns hidden,
- SelectionSource source, Object alignFrame)
- {
- return appLoader.getSelectionForListener(getCurrentAlignFrame(),
- seqsel, colsel, hidden, source, alignFrame);
- }
-
- @Override
- public String arrayToSeparatorList(String[] array)
- {
- return appLoader.arrayToSeparatorList(array);
- }
-
- @Override
- public Hashtable<String, int[]> getJSHashes()
- {
- return (jshashes == null ? (jshashes = new Hashtable<>())
- : jshashes);
- }
-
- @Override
- public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
- {
- return (jsmessages == null ? (jsmessages = new Hashtable<>())
- : jsmessages);
- }
-
- @Override
- public Object getFrameForSource(VamsasSource source)
- {
- if (source != null)
- {
- AlignFrame af;
- if (source instanceof jalview.gui.AlignViewport
- && source == (af = getCurrentAlignFrame()).getViewport())
- {
- // should be valid if it just generated an event!
- return af;
- }
- // TODO: ensure that if '_af' is specified along with a handler
- // function, then only events from that alignFrame are sent to that
- // function
- }
- return null;
- }
-
- @Override
- public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
- {
- return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
- }
-
- };
-
- appLoader = new JalviewAppLoader(true);
- appLoader.load(app);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
- */
- @Override
- public String getSelectedSequences()
- {
- return getSelectedSequencesFrom(getCurrentAlignFrame());
+ Jalview.getInstance().currentAlignFrame = currentAlignFrame;
}
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
- */
- @Override
- public String getSelectedSequences(String sep)
- {
- return getSelectedSequencesFrom(getCurrentAlignFrame(), sep);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame)
- */
- @Override
- public String getSelectedSequencesFrom(AlignFrame alf)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return getSelectedSequencesFrom(alf, null);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame, java.lang.String)
- */
- @Override
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getSelectedSequencesFrom(alf, sep);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame, java.lang.String)
- */
- @Override
- public void highlight(String sequenceId, String position,
- String alignedPosition)
- {
- highlightIn(null, sequenceId, position, alignedPosition);
- }
-
- @Override
- public void highlightIn(AlignFrame alf, String sequenceId,
- String position, String alignedPosition)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
- }
-
- @Override
- public void select(String sequenceIds, String columns)
- {
- selectIn(getCurrentAlignFrame(), sequenceIds, columns, null);
- }
-
- @Override
- public void select(String sequenceIds, String columns, String sep)
- {
- selectIn(null, sequenceIds, columns, sep);
- }
-
- @Override
- public void selectIn(AlignFrame alf, String sequenceIds, String columns)
- {
- selectIn(alf, sequenceIds, columns, null);
- }
-
- @Override
- public void selectIn(AlignFrame alf, String sequenceIds, String columns,
- String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.selectIn(alf, sequenceIds, columns, sep);
- }
-
- @Override
- public String getSelectedSequencesAsAlignment(String format,
- String suffix)
- {
- return getSelectedSequencesAsAlignmentFrom(null, format, suffix);
- }
-
- @Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
- }
-
- @Override
- public String getAlignmentOrder()
- {
- return getAlignmentFrom(getCurrentAlignFrame(), null);
- }
-
- @Override
- public String getAlignmentOrderFrom(AlignFrame alf)
- {
- return getAlignmentFrom(alf, null);
- }
-
- @Override
- public String getAlignmentOrderFrom(AlignFrame alf, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getAlignmentOrderFrom(alf, sep);
- }
-
- @Override
- public String orderBy(String order, String undoName)
- {
- return orderBy(order, undoName, null);
- }
-
- @Override
- public String orderBy(String order, String undoName, String sep)
- {
- return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep);
- }
-
- @Override
- public String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.orderAlignmentBy(alf, order, undoName, sep);
- }
-
- @Override
- public String getAlignment(String format)
- {
- return getAlignmentFrom(null, format, null);
- }
-
- @Override
- public String getAlignmentFrom(AlignFrame alf, String format)
- {
- return getAlignmentFrom(alf, format, null);
- }
-
- @Override
- public String getAlignment(String format, String suffix)
- {
- return getAlignmentFrom(getCurrentAlignFrame(), format, suffix);
- }
-
- @Override
- public String getAlignmentFrom(AlignFrame alf, String format,
- String suffix)
- {
- return appLoader.getAlignmentFrom(alf, format, suffix);
- }
-
- @Override
- public void loadAnnotation(String annotation)
- {
- loadAnnotationFrom(getCurrentAlignFrame(), annotation);
- }
-
- @Override
- public void loadAnnotationFrom(AlignFrame alf, String annotation)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.loadAnnotationFrom(alf, annotation);
- }
-
- @Override
- public void loadFeatures(String features, boolean autoenabledisplay)
- {
- loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
- }
-
- @Override
- public boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
- }
-
- @Override
- public String getFeatures(String format)
- {
- return getFeaturesFrom(null, format);
- }
-
- @Override
- public String getFeaturesFrom(AlignFrame alf, String format)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getFeaturesFrom(alf, format);
- }
-
- @Override
- public String getAnnotation()
- {
- return getAnnotationFrom(null);
- }
-
- @Override
- public String getAnnotationFrom(AlignFrame alf)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getAnnotationFrom(alf);
- }
-
- // @Override
- // public AlignFrame newView()
- // {
- // return newViewFrom(null, null);
- // }
- //
- // @Override
- // public AlignFrame newView(String name)
- // {
- // return newViewFrom(null, name);
- // }
- //
- // @Override
- // public AlignFrame newViewFrom(AlignFrame alf)
- // {
- // return newViewFrom(alf, null);
- // }
- //
- // @Override
- // public AlignFrame newViewFrom(AlignFrame alf, String name)
- // {
- // if (alf == null)
- // {
- // alf = getCurrentAlignFrame();
- // }
- // return appLoader.newViewFrom(alf, name);
- // }
-
- @Override
- public AlignFrame loadAlignment(String text, String title)
- {
- return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT, title);
- }
-
- @Override
- public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
- String pdbEntryString, String pdbFile)
- {
- if (alFrame == null)
- {
- alFrame = getCurrentAlignFrame();
- }
- return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
- pdbFile);
- }
-
- @Override
- public void scrollViewToIn(AlignFrame alf, String topRow,
- String leftHandColumn)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
- }
-
- @Override
- public void scrollViewToRowIn(AlignFrame alf, String topRow)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.scrollViewToRowIn(alf, topRow);
- }
-
- @Override
- public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.scrollViewToColumnIn(alf, leftHandColumn);
- }
-
- @Override
- public String getFeatureGroups()
- {
- return getFeatureGroupsOn(null);
- }
-
- @Override
- public String getFeatureGroupsOn(AlignFrame alf)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getFeatureGroupsOn(alf);
- }
-
- @Override
- public String getFeatureGroupsOfState(boolean visible)
- {
- return getFeatureGroupsOfStateOn(null, visible);
- }
-
- @Override
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getFeatureGroupsOfStateOn(alf, visible);
- }
-
- @Override
- public void setFeatureGroupState(String groups, boolean state)
- { // JalviewLite API
- setFeatureGroupStateOn(null, groups, state);
- }
-
- @Override
- public void setFeatureGroupStateOn(AlignFrame alf, String groups,
- boolean state)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.setFeatureGroupStateOn(alf, groups, state);
- }
-
- @Override
- public String getSeparator()
- {
- return appLoader.getSeparator();
- }
-
- @Override
- public void setSeparator(String separator)
- {
- appLoader.setSeparator(separator);
- }
-
- @Override
- public String getJsMessage(String messageclass, String viewId)
- {
- // see http://www.jalview.org/examples/jalviewLiteJs.html
- return null;
- }
-
- /**
- * Open a new Tree panel on the desktop statically. Params are standard (not
- * set by Groovy). No dialog is opened.
- *
- * @param af
- * @param treeType
- * @param modelName
- * @return null, or the string "label.you_need_at_least_n_sequences" if number
- * of sequences selected is inappropriate
- */
- @Override
- public Object openTreePanel(AlignFrame af, String treeType,
- String modelName)
- { // JalviewJS api
- if (af == null)
- {
- af = getCurrentAlignFrame();
- }
- return CalculationChooser.openTreePanel(af, treeType, modelName, null);
- }
-
- /**
- * public static method for JalviewJS API to open a PCAPanel without
- * necessarily using a dialog.
- *
- * @param af
- * @param modelName
- * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
- * if number of sequences selected is inappropriate
- */
- @Override
- public Object openPcaPanel(AlignFrame af, String modelName)
- {
- if (af == null)
- {
- af = getCurrentAlignFrame();
- }
- return CalculationChooser.openPcaPanel(af, modelName, null);
- }
-
- @Override
- public String getSelectedSequencesAsAlignment(String format,
- boolean suffix)
- {
- return getSelectedSequencesAsAlignmentFrom(null, format, suffix);
- }
-
- @Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, boolean suffix)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
- "" + suffix);
- }
-
- @Override
- public String arrayToSeparatorList(String[] array)
- {
- return appLoader.arrayToSeparatorList(array);
- }
-
- @Override
- public String[] separatorListToArray(String list)
- {
- return appLoader.separatorListToArray(list);
- }
-
- //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
- //// have a direct connection?
-
- @Override
- public void setMouseoverListener(String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setMouseoverListener(AlignFrame af, String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setSelectionListener(String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setSelectionListener(AlignFrame af, String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setStructureListener(String listener, String modelSet)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void removeJavascriptListener(AlignFrame af, String listener)
+
+ public void notifyWorker(AlignCalcWorkerI worker, String status)
{
- // TODO Auto-generated method stub
-
+ // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+ // + " " + status);
}
- @Override
- public void mouseOverStructure(String pdbResNum, String chain,
- String pdbfile)
- {
- // TODO Auto-generated method stub
- }
+ private static boolean isInteractive = true;
- @Override
- public void showOverview()
+ public static boolean isInteractive()
{
- currentAlignFrame.overviewMenuItem_actionPerformed(null);
+ return isInteractive;
}
- public void notifyWorker(AlignCalcWorkerI worker, String status)
+ public static void setInteractive(boolean tf)
{
- // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
- // + " " + status);
+ isInteractive = tf;
}
}
git://source.jalview.org / jalview.git / blobdiff